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Barrera FN. On 'Fourier transform infrared study of proteins with parallel β-chains' by Heino Susi, D. Michael Byler. Arch Biochem Biophys 2022; 726:109114. [PMID: 34973205 DOI: 10.1016/j.abb.2021.109114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 11/24/2022]
Abstract
In 1987, Susi & Byler published a groundbreaking paper for the determination of the secondary structure of proteins. Notably, they determined the characteristic signature of the β-strand in the infrared spectrum. As a result, Fourier-transform infrared spectroscopy became a general method to determine protein structure.
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Affiliation(s)
- Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee Knoxville, USA.
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2
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Garcia-Alles LF, Root K, Maveyraud L, Aubry N, Lesniewska E, Mourey L, Zenobi R, Truan G. Occurrence and stability of hetero-hexamer associations formed by β-carboxysome CcmK shell components. PLoS One 2019; 14:e0223877. [PMID: 31603944 PMCID: PMC6788708 DOI: 10.1371/journal.pone.0223877] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022] Open
Abstract
The carboxysome is a bacterial micro-compartment (BMC) subtype that encapsulates enzymatic activities necessary for carbon fixation. Carboxysome shells are composed of a relatively complex cocktail of proteins, their precise number and identity being species dependent. Shell components can be classified in two structural families, the most abundant class associating as hexamers (BMC-H) that are supposed to be major players for regulating shell permeability. Up to recently, these proteins were proposed to associate as homo-oligomers. Genomic data, however, demonstrated the existence of paralogs coding for multiple shell subunits. Here, we studied cross-association compatibilities among BMC-H CcmK proteins of Synechocystis sp. PCC6803. Co-expression in Escherichia coli proved a consistent formation of hetero-hexamers combining CcmK1 and CcmK2 or, remarkably, CcmK3 and CcmK4 subunits. Unlike CcmK1/K2 hetero-hexamers, the stoichiometry of incorporation of CcmK3 in associations with CcmK4 was low. Cross-interactions implicating other combinations were weak, highlighting a structural segregation of the two groups that could relate to gene organization. Sequence analysis and structural models permitted the localization of interactions that would favor formation of CcmK3/K4 hetero-hexamers. The crystallization of these CcmK3/K4 associations conducted to the elucidation of a structure corresponding to the CcmK4 homo-hexamer. Yet, subunit exchange could not be demonstrated in vitro. Biophysical measurements showed that hetero-hexamers are thermally less stable than homo-hexamers, and impeded in forming larger assemblies. These novel findings are discussed within the context of reported data to propose a functional scenario in which minor CcmK3/K4 incorporation in shells would introduce sufficient local disorder as to allow shell remodeling necessary to adapt rapidly to environmental changes.
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Affiliation(s)
- Luis F. Garcia-Alles
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- * E-mail:
| | - Katharina Root
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Laurent Maveyraud
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nathalie Aubry
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Eric Lesniewska
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Lionel Mourey
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Gilles Truan
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
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Miyazaki Y, Miyake A, Doi N, Koma T, Uchiyama T, Adachi A, Nomaguchi M. Comparison of Biochemical Properties of HIV-1 and HIV-2 Capsid Proteins. Front Microbiol 2017; 8:1082. [PMID: 28659897 PMCID: PMC5469281 DOI: 10.3389/fmicb.2017.01082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/29/2017] [Indexed: 01/08/2023] Open
Abstract
Timely disassembly of viral core composed of self-assembled capsid (CA) in infected host cells is crucial for retroviral replication. Extensive in vitro studies to date on the self-assembly/disassembly mechanism of human immunodeficiency virus type 1 (HIV-1) CA have revealed its core structure and amino acid residues essential for CA–CA intermolecular interaction. However, little is known about in vitro properties of HIV-2 CA. In this study, we comparatively analyzed the polymerization properties of bacterially expressed HIV-1 and HIV-2 CA proteins. Interestingly, a much higher concentration of NaCl was required for HIV-2 CA to self-assemble than that for HIV-1 CA, but once the polymerization started, the reaction proceeded more rapidly than that observed for HIV-1 CA. Analysis of a chimeric protein revealed that N-terminal domain (NTD) is responsible for this unique property of HIV-2 CA. To further study the molecular basis for different in vitro properties of HIV-1 and HIV-2 CA proteins, we determined thermal stabilities of HIV-1 and HIV-2 CA NTD proteins at several NaCl concentrations by fluorescent-based thermal shift assays. Experimental data obtained showed that HIV-2 CA NTD was structurally more stable than HIV-1 CA NTD. Taken together, our results imply that distinct in vitro polymerization abilities of the two CA proteins are related to their structural instability/stability, which is one of the decisive factors for viral replication potential. In addition, our assay system described here may be potentially useful for searching for anti-CA antivirals against HIV-1 and HIV-2.
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Affiliation(s)
- Yasuyuki Miyazaki
- Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical ScienceTokyo, Japan
| | - Ariko Miyake
- Laboratory of Molecular Immunology and Infectious Disease, Joint Faculty of Veterinary Medicine, Yamaguchi UniversityYamaguchi, Japan
| | - Noya Doi
- Department of Microbiology, Tokushima University Graduate School of Medical SciencesTokushima, Japan
| | - Takaaki Koma
- Department of Microbiology, Tokushima University Graduate School of Medical SciencesTokushima, Japan
| | - Tsuneo Uchiyama
- Department of Microbiology, Tokushima University Graduate School of Medical SciencesTokushima, Japan
| | - Akio Adachi
- Department of Microbiology, Tokushima University Graduate School of Medical SciencesTokushima, Japan
| | - Masako Nomaguchi
- Department of Microbiology, Tokushima University Graduate School of Medical SciencesTokushima, Japan
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Garg DK, Kundu B. Hyperthermophilic l -asparaginase bypasses monomeric intermediates during folding to retain cooperativity and avoid amyloid assembly. Arch Biochem Biophys 2017; 622:36-46. [DOI: 10.1016/j.abb.2017.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 10/19/2022]
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Qiao X, Jeon J, Weber J, Zhu F, Chen B. Mechanism of polymorphism and curvature of HIV capsid assemblies probed by 3D simulations with a novel coarse grain model. Biochim Biophys Acta Gen Subj 2015; 1850:2353-67. [PMID: 26318016 DOI: 10.1016/j.bbagen.2015.08.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/17/2015] [Accepted: 08/19/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND During the maturation process, HIV capsid proteins self-assemble into polymorphic capsids. The strong polymorphism precludes high resolution structural characterization under in vivo conditions. In spite of the determination of structural models for various in vitro assemblies of HIV capsid proteins, the assembly mechanism is still not well-understood. METHODS We report 3D simulations of HIV capsid proteins by a novel coarse grain model that captures the backbone of the rigid segments in the protein accurately. The effects of protein dynamics on assembly are emulated by a static ensemble of subunits in conformations derived from molecular dynamics simulation. RESULTS We show that HIV capsid proteins robustly assemble into hexameric lattices in a range of conditions where trimers of dimeric subunits are the dominant oligomeric intermediates. Variations of hexameric lattice curvatures are observed in simulations with subunits of variable inter-domain orientations mimicking the conformation distribution in solution. Simulations with subunits based on pentameric structural models lead to assembly of sharp curved structures resembling the tips of authentic HIV capsids, along a distinct pathway populated by tetramers and pentamers with the characteristic quasi-equivalency of viral capsids. CONCLUSIONS Our results suggest that the polymorphism assembly is triggered by the inter-domain dynamics of HIV capsid proteins in solution. The assembly of highly curved structures arises from proteins in conformation with a highly specific inter-domain orientation. SIGNIFICANCE Our work proposes a mechanism of HIV capsid assembly based on available structural data, which can be readily verified. Our model can be applied to other large biomolecular assemblies.
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Affiliation(s)
- Xin Qiao
- Department of Physics, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA
| | - Jaekyun Jeon
- Department of Physics, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA
| | - Jeff Weber
- Department of Physics, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA
| | - Fangqiang Zhu
- Department of Physics, Indiana University - Purdue University Indianapolis, IN, USA
| | - Bo Chen
- Department of Physics, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
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Abstract
I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to molecular dynamics simulations, and I give an overview of some of the important conclusions about virus assembly that have resulted from these modeling efforts. Topics include the assembly of empty viral shells, assembly around single-stranded nucleic acids to form viral particles, and assembly around synthetic polymers or charged nanoparticles for nanotechnology or biomedical applications. I present some examples in which modeling efforts have promoted experimental breakthroughs, as well as directions in which the connection between modeling and experiment can be strengthened.
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Oligomerization, conformational stability and thermal unfolding of Harpin, HrpZPss and its hypersensitive response-inducing c-terminal fragment, C-214-HrpZPss. PLoS One 2014; 9:e109871. [PMID: 25502017 PMCID: PMC4264689 DOI: 10.1371/journal.pone.0109871] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 09/04/2014] [Indexed: 11/19/2022] Open
Abstract
HrpZ-a harpin from Pseudomonas syringae-is a highly thermostable protein that exhibits multifunctional abilities e.g., it elicits hypersensitive response (HR), enhances plant growth, acts as a virulence factor, and forms pores in plant plasma membranes as well as artificial membranes. However, the molecular mechanism of its biological activity and high thermal stability remained poorly understood. HR inducing abilities of non-overlapping short deletion mutants of harpins put further constraints on the ability to establish structure-activity relationships. We characterized HrpZPss from Pseudomonas syringae pv. syringae and its HR inducing C-terminal fragment with 214 amino acids (C-214-HrpZPss) using calorimetric, spectroscopic and microscopic approaches. Both C-214-HrpZPss and HrpZPss were found to form oligomers. We propose that leucine-zipper-like motifs may take part in the formation of oligomeric aggregates, and oligomerization could be related to HR elicitation. CD, DSC and fluorescence studies showed that the thermal unfolding of these proteins is complex and involves multiple steps. The comparable conformational stability at 25°C (∼10.0 kcal/mol) of HrpZPss and C-214-HrpZPss further suggest that their structures are flexible, and the flexibility allows them to adopt proper conformation for multifunctional abilities.
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Conformational stability and activity analysis of two hydroxymethylbilane synthase mutants, K132N and V215E, with different phenotypic association with acute intermittent porphyria. Biosci Rep 2013; 33:BSR20130045. [PMID: 23815679 PMCID: PMC3738108 DOI: 10.1042/bsr20130045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The autosomal dominantly inherited disease AIP (acute intermittent porphyria) is caused by mutations in HMBS [hydroxymethylbilane synthase; also known as PBG (porphobilinogen) deaminase], the third enzyme in the haem biosynthesis pathway. Enzyme-intermediates with increasing number of PBG molecules are formed during the catalysis of HMBS. In this work, we studied the two uncharacterized mutants K132N and V215E comparative with wt (wild-type) HMBS and to the previously reported AIP-associated mutants R116W, R167W and R173W. These mainly present defects in conformational stability (R116W), enzyme kinetics (R167W) or both (R173W). A combination of native PAGE, CD, DSF (differential scanning fluorimetry) and ion-exchange chromatography was used to study conformational stability and activity of the recombinant enzymes. We also investigated the distribution of intermediates corresponding to specific elongation stages. It is well known that the thermostability of HMBS increases when the DPM (dipyrromethane) cofactor binds to the apoenzyme and the holoenzyme is formed. Interestingly, a decrease in thermal stability was measured concomitant to elongation of the pyrrole chain, indicating a loosening of the structure prior to product release. No conformational or kinetic defect was observed for the K132N mutant, whereas V215E presented lower conformational stability and probably a perturbed elongation process. This is in accordance with the high association of V215E with AIP. Our results contribute to interpret the molecular mechanisms for dysfunction of HMBS mutants and to establish genotype–phenotype relations for AIP.
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Lampel A, Bram Y, Levy-Sakin M, Bacharach E, Gazit E. The effect of chemical chaperones on the assembly and stability of HIV-1 capsid protein. PLoS One 2013; 8:e60867. [PMID: 23577173 PMCID: PMC3618117 DOI: 10.1371/journal.pone.0060867] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 03/04/2013] [Indexed: 11/18/2022] Open
Abstract
Chemical chaperones are small organic molecules which accumulate in a broad range of organisms in various tissues under different stress conditions and assist in the maintenance of a correct proteostasis under denaturating environments. The effect of chemical chaperones on protein folding and aggregation has been extensively studied and is generally considered to be mediated through non-specific interactions. However, the precise mechanism of action remains elusive. Protein self-assembly is a key event in both native and pathological states, ranging from microtubules and actin filaments formation to toxic amyloids appearance in degenerative disorders, such as Alzheimer's and Parkinson's diseases. Another pathological event, in which protein assembly cascade is a fundamental process, is the formation of virus particles. In the late stage of the virus life cycle, capsid proteins self-assemble into highly-ordered cores, which encapsulate the viral genome, consequently protect genome integrity and mediate infectivity. In this study, we examined the effect of different groups of chemical chaperones on viral capsid assembly in vitro, focusing on HIV-1 capsid protein as a system model. We found that while polyols and sugars markedly inhibited capsid assembly, methylamines dramatically enhanced the assembly rate. Moreover, chemical chaperones that inhibited capsid core formation, also stabilized capsid structure under thermal denaturation. Correspondingly, trimethylamine N-oxide, which facilitated formation of high-order assemblies, clearly destabilized capsid structure under similar conditions. In contrast to the prevailing hypothesis suggesting that chemical chaperones affect proteins through preferential exclusion, the observed dual effects imply that different chaperones modify capsid assembly and stability through different mechanisms. Furthermore, our results indicate a correlation between the folding state of capsid to its tendency to assemble into highly-ordered structures.
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Affiliation(s)
- Ayala Lampel
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Yaron Bram
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Michal Levy-Sakin
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bacharach
- Department of Cell Research and Immunology, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (EB); (EG)
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (EB); (EG)
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10
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Simulations of HIV capsid protein dimerization reveal the effect of chemistry and topography on the mechanism of hydrophobic protein association. Biophys J 2013; 103:1363-9. [PMID: 22995509 DOI: 10.1016/j.bpj.2012.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 07/31/2012] [Accepted: 08/06/2012] [Indexed: 01/17/2023] Open
Abstract
Recent work has shown that the hydrophobic protein surfaces in aqueous solution sit near a drying transition. The tendency for these surfaces to expel water from their vicinity leads to self-assembly of macromolecular complexes. In this article, we show with a realistic model for a biologically pertinent system how this phenomenon appears at the molecular level. We focus on the association of the C-terminal domain (CA-C) of the human immunodeficiency virus capsid protein. By combining all-atom simulations with specialized sampling techniques, we measure the water density distribution during the approach of two CA-C proteins as a function of separation and amino acid sequence in the interfacial region. The simulations demonstrate that CA-C protein-protein interactions sit at the edge of a dewetting transition and that this mesoscopic manifestation of the underlying liquid-vapor phase transition can be readily manipulated by biology or protein engineering to significantly affect association behavior. Although the wild-type protein remains wet until contact, we identify a set of in silico mutations, in which three hydrophilic amino acids are replaced with nonpolar residues, that leads to dewetting before association. The existence of dewetting depends on the size and relative locations of substituted residues separated by nanometer length scales, indicating long-range cooperativity and a sensitivity to surface topography. These observations identify important details that are missing from descriptions of protein association based on buried hydrophobic surface area.
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11
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Boonyalai N, Pullen JR, Abdul Wahab MF, Wright M, Miller AD. Escherichia coli LysU is a potential surrogate for human lysyl tRNA synthetase in interactions with the C-terminal domain of HIV-1 capsid protein. Org Biomol Chem 2013. [DOI: 10.1039/c2ob26499d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Doyle CM, Rumfeldt JA, Broom HR, Broom A, Stathopulos PB, Vassall KA, Almey JJ, Meiering EM. Energetics of oligomeric protein folding and association. Arch Biochem Biophys 2012; 531:44-64. [PMID: 23246784 DOI: 10.1016/j.abb.2012.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/29/2012] [Accepted: 12/05/2012] [Indexed: 12/11/2022]
Abstract
In nature, proteins most often exist as complexes, with many of these consisting of identical subunits. Understanding of the energetics governing the folding and misfolding of such homooligomeric proteins is central to understanding their function and misfunction, in disease or biotechnology. Much progress has been made in defining the mechanisms and thermodynamics of homooligomeric protein folding. In this review, we outline models as well as calorimetric and spectroscopic methods for characterizing oligomer folding, and describe extensive results obtained for diverse proteins, ranging from dimers to octamers and higher order aggregates. To our knowledge, this area has not been reviewed comprehensively in years, and the collective progress is impressive. The results provide evolutionary insights into the development of subunit interfaces, mechanisms of oligomer folding, and contributions of oligomerization to protein stability, function and regulation. Thermodynamic analyses have also proven valuable for understanding protein misfolding and aggregation mechanisms, suggesting new therapeutic avenues. Successful recent designs of novel, functional proteins demonstrate increased understanding of oligomer folding. Further rigorous analyses using multiple experimental and computational approaches are still required, however, to achieve consistent and accurate prediction of oligomer folding energetics. Modeling the energetics remains challenging but is a promising avenue for future advances.
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Affiliation(s)
- Colleen M Doyle
- Guelph-Waterloo Centre for Graduate Studies in Chemistry and Biochemistry, and Department of Chemistry, University of Waterloo, 200 University Ave. West, Waterloo, ON, Canada
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Chen B, Tycko R. Structural and dynamical characterization of tubular HIV-1 capsid protein assemblies by solid state nuclear magnetic resonance and electron microscopy. Protein Sci 2010; 19:716-30. [PMID: 20095046 DOI: 10.1002/pro.348] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The wild-type HIV-1 capsid protein (CA) self-assembles in vitro into tubular structures at high ionic strength. We report solid state nuclear magnetic resonance (NMR) and electron microscopy measurements on these tubular CA assemblies, which are believed to contain a triangular lattice of hexameric CA proteins that is similar or identical to the lattice of capsids in intact HIV-1. Mass-per-length values of CA assemblies determined by dark-field transmission electron microscopy indicate a variety of structures, ranging from single-wall tubes to multiwall tubes that approximate solid rods. Two-dimensional (2D) solid state (13)C--(13)C and (15)N--(13)C NMR spectra of uniformly (15)N,(13)C-labeled CA assemblies are highly congested, as expected for a 25.6 kDa protein in which nearly the entire amino acid sequence is immobilized. Solid state NMR spectra of partially labeled CA assemblies, expressed in 1,3-(13)C(2)-glycerol medium, are better resolved, allowing the identification of individual signals with line widths below 1 ppm. Comparison of crosspeak patterns in the experimental 2D spectra with simulated patterns based on solution NMR chemical shifts of the individual N-terminal (NTD) and C-terminal (CTD) domains indicates that NTD and CTD retain their individual structures upon self-assembly of full-length CA into tubes. 2D (1)H-(13)C NMR spectra of CA assemblies recorded under solution NMR conditions show relatively few signals, primarily from segments that link the alpha-helices of NTD and CTD and from the N- and C-terminal ends. Taken together, the data support the idea that CA assemblies contain a highly ordered 2D protein lattice in which the NTD and CTD structures are retained and largely immobilized.
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Affiliation(s)
- Bo Chen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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14
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Doménech R, Abian O, Bocanegra R, Correa J, Sousa-Herves A, Riguera R, Mateu MG, Fernandez-Megia E, Velázquez-Campoy A, Neira JL. Dendrimers as Potential Inhibitors of the Dimerization of the Capsid Protein of HIV-1. Biomacromolecules 2010; 11:2069-78. [DOI: 10.1021/bm100432x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Rosa Doménech
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Olga Abian
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Rebeca Bocanegra
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Juan Correa
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Ana Sousa-Herves
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Ricardo Riguera
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Mauricio G. Mateu
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Eduardo Fernandez-Megia
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Adrián Velázquez-Campoy
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - José L. Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
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15
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Mateu MG. The capsid protein of human immunodeficiency virus: intersubunit interactions during virus assembly. FEBS J 2009; 276:6098-109. [DOI: 10.1111/j.1742-4658.2009.07313.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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16
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Yu X, Wang Q, Yang JC, Buch I, Tsai CJ, Ma B, Cheng SZD, Nussinov R, Zheng J. Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain. Biomacromolecules 2009; 10:390-9. [PMID: 19199580 PMCID: PMC2651736 DOI: 10.1021/bm801151r] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The carboxyl-terminal domain (CTD, residues 146-231) of the HIV-1 capsid (CA) protein plays an important role in the CA-CA dimerization and viral assembly of the human immunodeficiency virus type 1. Disrupting the native conformation of the CA is essential for blocking viral capsid formation and viral replication. Thus, it is important to identify the exact nature of the structural changes and driving forces of the CTD dimerization that take place in mutant forms. Here, we compare the structural stability, conformational dynamics, and association force of the CTD dimers for both wild-type and mutated sequences using all-atom explicit-solvent molecular dynamics (MD). The simulations show that Q155N and E159D at the major homology region (MHR) and W184A and M185A at the helix 2 region are energetically less favorable than the wild-type, imposing profound negative effects on intermolecular CA-CA dimerization. Detailed structural analysis shows that three mutants (Q155N, E159D, and W184A) display much more flexible local structures and weaker CA-CA association than the wildtype, primarily due to the loss of interactions (hydrogen bonds, side chain hydrophobic contacts, and pi-stacking) with their neighboring residues. Most interestingly, the MHR that is far from the interacting dimeric interface is more sensitive to the mutations than the helix 2 region that is located at the CA-CA dimeric interface, indicating that structural changes in the distinct motif of the CA could similarly allosterically prevent the CA capsid formation. In addition, the structural and free energy comparison of the five residues shorter CA (151-231) dimer with the CA (146-231) dimer further indicates that hydrophobic interactions, side chain packing, and hydrogen bonds are the major, dominant driving forces in stabilizing the CA interface.
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Affiliation(s)
- Xiang Yu
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
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17
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Mark J, Li X, Cyr T, Fournier S, Jaentschke B, Hefford MA. SARS coronavirus: unusual lability of the nucleocapsid protein. Biochem Biophys Res Commun 2008; 377:429-433. [PMID: 18926799 PMCID: PMC7092863 DOI: 10.1016/j.bbrc.2008.09.153] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Accepted: 09/30/2008] [Indexed: 01/30/2023]
Abstract
The severe acute respiratory syndrome (SARS) is a contagious disease that killed hundreds and sickened thousands of people worldwide between November 2002 and July 2003. The nucleocapsid (N) protein of the coronavirus responsible for this disease plays a critical role in viral assembly and maturation and is of particular interest because of its potential as an antiviral target or vaccine candidate. Refolding of SARS N-protein during production and purification showed the presence of two additional protein bands by SDS-PAGE. Mass spectroscopy (MALDI, SELDI, and LC/MS) confirmed that the bands are proteolytic products of N-protein and the cleavage sites are four SR motifs in the serine-arginine-rich region-sites not suggestive of any known protease. Furthermore, results of subsequent testing for contaminating protease(s) were negative: cleavage appears to be due to inherent instability and/or autolysis. The importance of N-protein proteolysis to viral life cycle and thus to possible treatment directions are discussed.
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Affiliation(s)
- John Mark
- Centre for Biologics Research, Biologics and Genetic Therapies Directorate, Health Canada, 251 Sir Frederick Banting Driveway, AL:2201E, Ottawa, Ont., Canada K1A 0L2
| | - Xuguang Li
- Centre for Biologics Research, Biologics and Genetic Therapies Directorate, Health Canada, 251 Sir Frederick Banting Driveway, AL:2201E, Ottawa, Ont., Canada K1A 0L2
| | - Terry Cyr
- Centre for Biologics Research, Biologics and Genetic Therapies Directorate, Health Canada, 251 Sir Frederick Banting Driveway, AL:2201E, Ottawa, Ont., Canada K1A 0L2
| | - Sylvie Fournier
- Centre for Biologics Research, Biologics and Genetic Therapies Directorate, Health Canada, 251 Sir Frederick Banting Driveway, AL:2201E, Ottawa, Ont., Canada K1A 0L2
| | - Bozena Jaentschke
- Centre for Biologics Research, Biologics and Genetic Therapies Directorate, Health Canada, 251 Sir Frederick Banting Driveway, AL:2201E, Ottawa, Ont., Canada K1A 0L2
| | - Mary Alice Hefford
- Centre for Biologics Research, Biologics and Genetic Therapies Directorate, Health Canada, 251 Sir Frederick Banting Driveway, AL:2201E, Ottawa, Ont., Canada K1A 0L2.
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18
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Alcaraz LA, Del Alamo M, Mateu MG, Neira JL. Structural mobility of the monomeric C-terminal domain of the HIV-1 capsid protein. FEBS J 2008; 275:3299-311. [PMID: 18489586 DOI: 10.1111/j.1742-4658.2008.06478.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The capsid protein of HIV-1 (p24) (CA) forms the mature capsid of the human immunodeficiency virus. Capsid assembly involves hexamerization of the N-terminal domain and dimerization of the C-terminal domain of CA (CAC), and both domains constitute potential targets for anti-HIV therapy. CAC homodimerization occurs mainly through its second helix, and it is abolished when its sole tryptophan is mutated to alanine. This mutant, CACW40A, resembles a transient monomeric intermediate formed during dimerization. Its tertiary structure is similar to that of the subunits in the dimeric, non-mutated CAC, but the segment corresponding to the second helix samples different conformations. The present study comprises a comprehensive examination of the CACW40A internal dynamics. The results obtained, with movements sampling a wide time regime (from pico- to milliseconds), demonstrate the high flexibility of the whole monomeric protein. The conformational exchange phenomena on the micro-to-millisecond time scale suggest a role for internal motions in the monomer-monomer interactions and, thus, flexibility of the polypeptide chain is likely to contribute to the ability of the protein to adopt different conformational states, depending on the biological environment.
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Affiliation(s)
- Luis A Alcaraz
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche (Alicante), Spain
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19
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Alcaraz LA, del Alamo M, Barrera FN, Mateu MG, Neira JL. Flexibility in HIV-1 assembly subunits: solution structure of the monomeric C-terminal domain of the capsid protein. Biophys J 2007; 93:1264-76. [PMID: 17526561 PMCID: PMC1929042 DOI: 10.1529/biophysj.106.101089] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The protein CA forms the mature capsid of human immunodeficiency virus. Hexamerization of the N-terminal domain and dimerization of the C-terminal domain, CAC, occur during capsid assembly, and both domains constitute potential targets for anti-HIV inhibitors. CAC homodimerization occurs mainly through its second helix, and is abolished when its sole tryptophan is mutated to alanine. Previous thermodynamic data obtained with the dimeric and monomeric forms of CAC indicate that the structure of the mutant resembles that of a monomeric intermediate found in the folding and association reactions of CAC. We have solved the three-dimensional structure in aqueous solution of the monomeric mutant. The structure is similar to that of the subunits in the dimeric, nonmutated CAC, except the segment corresponding to the second helix, which is highly dynamic. At the end of this region, the polypeptide chain is bent to bury several hydrophobic residues and, as a consequence, the last two helices are rotated 90 degrees when compared to their position in dimeric CAC. The previously obtained thermodynamic data are consistent with the determined structure of the monomeric mutant. This extraordinary ability of CAC to change its structure may contribute to the different modes of association of CA during HIV assembly, and should be taken into account in the design of new drugs against this virus.
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Affiliation(s)
- Luis A Alcaraz
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche (Alicante), Spain
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20
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Barrera F, Hurtado-Gómez E, Lidón-Moya M, Neira J. Binding of the C-terminal domain of the HIV-1 capsid protein to lipid membranes: a biophysical characterization. Biochem J 2006; 394:345-53. [PMID: 16259620 PMCID: PMC1386033 DOI: 10.1042/bj20051487] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The capsid protein, CA, of HIV-1 forms a capsid that surrounds the viral genome. However, recent studies have shown that an important proportion of the CA molecule does not form part of this capsid, and its location and function are still unknown. In the present work we show, by using fluorescence, differential scanning calorimetry and Fourier-transform infrared spectroscopy, that the C-terminal region of CA, CA-C, is able to bind lipid vesicles in vitro in a peripheral fashion. CA-C had a greater affinity for negatively charged lipids (phosphatidic acid and phosphatidylserine) than for zwitterionic lipids [PC/Cho/SM (equimolar mixture of phosphatidylcholine, cholesterol and sphingomyelin) and phosphatidylcholine]. The interaction of CA-C with lipid membranes was supported by theoretical studies, which predicted that different regions, occurring close in the three-dimensional CA-C structure, were responsible for the binding. These results show the flexibility of CA-C to undergo conformational rearrangements in the presence of different binding partners. We hypothesize that the CA molecules that do not form part of the mature capsid might be involved in lipid-binding interactions in the inner leaflet of the virion envelope.
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Affiliation(s)
- Francisco N. Barrera
- *Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
- To whom correspondence should be addressed (email and )
| | - Estefanía Hurtado-Gómez
- *Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - María C. Lidón-Moya
- *Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - José L. Neira
- *Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
- †Biocomputation and Complex Systems Physics Institute, 50009 Zaragoza, Spain
- To whom correspondence should be addressed (email and )
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